Quantitative information regarding the capacity of rivers to self-purify pharmaceutical residues is limited. To bridge this knowledge gap, we present a methodology for quantifying the governing processes affecting the fate of pharmaceuticals in streaming waters and, especially, to evaluate their relative significance for tracer observations. A tracer test in Sava Brook, Sweden was evaluated using a coupled physical-biogeochemical model framework containing surface water transport together with a representation of transient storage in slow/immobile zones of the stream, which are presumably important for the retention and attenuation of pharmaceuticals. To assess the key processes affecting the environmental fate of the compounds, we linked the uncertainty estimates of the reaction rate coefficients to the relative influence of transformation and sorption that occurred in different stream environments. The hydrological and biogeochemical contributions to the fate of the pharmaceuticals were decoupled, and the results indicate a moderate hydrological retention in the hyporheic zone as well as in the densely vegetated parts of the stream. Biogeochemical reactions in these transient storage zones further affected the fate of the pharmaceuticals, and we found that sorption was the key process for bezafibrate, metoprolol, and naproxen, while primary transformation was the most important process for clofibric acid and ibuprofen. Conversely, diclofenac was not affected by sorption or transformation.